rs1547531

chr5-30796284-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.808 in 151,926 control chromosomes in the GnomAD database, including 49,900 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.81 (49900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122660 AN: 151810 Hom.: 49848 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.806

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.808 AC: 122771 AN: 151926 Hom.: 49900 Cov.: 31 AF XY: 0.809 AC XY: 60100 AN XY: 74246

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.807

Alfa AF: 0.782 Hom.: 21431

Bravo AF: 0.820

Asia WGS AF: 0.913 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.69
Dann	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1547531; hg19: chr5-30796391;